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	<title>Bekiyrah &#187; Science</title>
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		<title>23andMe and I</title>
		<link>http://juliesandburg.com/blog/2011/09/23andme-and-i/</link>
		<comments>http://juliesandburg.com/blog/2011/09/23andme-and-i/#comments</comments>
		<pubDate>Fri, 16 Sep 2011 15:00:47 +0000</pubDate>
		<dc:creator>Julie</dc:creator>
				<category><![CDATA[Health]]></category>
		<category><![CDATA[Life]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[Technology]]></category>

		<guid isPermaLink="false">http://juliesandburg.com/blog/?p=2178</guid>
		<description><![CDATA[Last month I was lucky enough to get a &#8220;friends and family&#8221; discount code last month for $50 off of 23andMe, a consumer genetics company offering very basic genotyping (thanks, Anthony!). What they look at are called SNPs, or snips—your genotypes, information at certain locations on your chromosomes you&#8217;ve received from your parents. What is [...]]]></description>
			<content:encoded><![CDATA[<p style="text-align: left;">Last month I was lucky enough to get a &#8220;friends and family&#8221; discount code last month for $50 off of <a href="http://23andme.com" target="_blank">23andMe</a>, a consumer genetics company offering very basic genotyping (thanks, <a title="Anthony C Maki" href="http://acmaki.com" target="_blank">Anthony</a>!). What they look at are called <a title="SNPedia" href="http://www.snpedia.com/index.php/Genotype" target="_blank">SNPs, or <em>snips</em></a><em>—</em>your genotypes, information at certain locations on your chromosomes you&#8217;ve received from your parents.</p>
<p style="text-align: left;">What is most valuable is the raw data, which is available for download in a non-proprietary format. Through using 3rd-party software with the raw data, I&#8217;ve been able to learn more than 23andMe reveals. (The raw data also comes in very handy if you&#8217;re not 100% European because 23andMe has a self-acknowledged Eurocentric model.)</p>
<p style="text-align: left;"><span id="more-2178"></span>For example, how <a title="Neanderthal admixture theory" href="http://en.wikipedia.org/wiki/Neanderthal_admixture_theory">Neanderthal</a> I am from <a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a>: 11 out of 84 identified Neanderthal SNPs. I like the little meter it uses.</p>
<p><img class="aligncenter size-medium wp-image-2181" title="Neanderthal" src="http://juliesandburg.com/blog/wp-content/uploads/2011/09/Screen-shot-2011-09-01-at-4.29.37-AM-250x248.png" alt="" width="175" height="174" /></p>
<p style="text-align: left;"><a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a> is a great resource for digging through your raw data since it involves using your browser, instead of downloading and installing something such as <a title="R Project" href="http://www.r-project.org/" target="_blank">R</a> and then running available scripts. Not everyone is comfortable with the latter so the Interpretome interface makes it highly recommended.</p>
<h4 style="text-align: left;">Some things I learned from 23andMe:</h4>
<ul>
<li>I&#8217;m 100% European.</li>
<li>My <a title="Human mitochondrial DNA haplogroup" href="http://en.wikipedia.org/wiki/Human_mitochondrial_DNA_haplogroup">mitochondrial DNA (mtDNA) haplogroup</a> is H11, from &#8220;Central Europe.&#8221;</li>
<li>Compared to average, I have nearly twice the risk for Alzheimer&#8217;s disease and about 1.5x the risk for Coronary Heart Disease, lung cancer, Restless Legs Syndrome, and ulcerative colitis.</li>
<li>I have an &#8220;increased risk&#8221; of gout and Chronic Obstructive Pulmonary Disease (COPD).</li>
<li>I&#8217;m not a carrier for any of the various things they tested for: Cystic Fibrosis, Tay-Sach&#8217;s, Connexin 26-related sensorineural hearing loss, etc.</li>
<li>I am norovirus-resistant.</li>
<li>My blood type is likely B (it&#8217;s B positive).</li>
<li>My eyes are likely brown (they&#8217;re green).</li>
<li>I&#8217;m not resistant to HIV/AIDS.</li>
</ul>
<h4 style="text-align: left;">Some things I learned from the raw data + third parties:</h4>
<ul>
<li>I have 19 &#8220;European alleles&#8221; and 1 &#8220;East Asian allele,&#8221; whatever that means. (<a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a>)</li>
<li>At maximum: my ancestry is 93% Northwestern European, 7% Southeastern European, 0% Ashkenazi Jewish. (<a title="Euro-DNA-Calc" href="http://dienekes.blogspot.com/2008/06/euro-dna-calc-11-released.html" target="_blank">Euro-DNA-Calc</a>)</li>
<li>I have 11 out of 84 identified Neanderthal SNPs (as seen above from <a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a>)</li>
<li>From Doug McDonald&#8217;s BGA Project (search the 23andMe forums for his email address):<br />
<blockquote><p>Most likely fit is 43.0% (+-  6.4%) Europe (various subcontinents) and 57.0% (+-  6.4%) Europe (all Northeast Europe), which is 100% total Europe. The following are possible population sets and their fractions, most likely at the top.</p>
<p>Italian= 0.386 Lithuani= 0.614<br />
Spain= 0.381 Lithuani= 0.619<br />
French= 0.538 Lithuani= 0.462<br />
French= 0.416 Belorus= 0.584</p>
<p>For some reason the above and the <a href="http://juliesandburg.com/blog/wp-content/uploads/2011/09/Julie_Sandburg_Full_20110830232845BGA2.png" target="_blank">spot on the map</a>, which both look like Germany, seem to contradict the <a href="http://juliesandburg.com/blog/wp-content/uploads/2011/09/Julie_Sandburg_Full_20110830232845BGA3.png" target="_blank">scatter plot</a>, which looks quite like plain England. So I would say that it could be anywhere from England to Germany.</p></blockquote>
</li>
<li>I have 21 out of 32 Coronary Artery Disease risk alleles. (<a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a>)</li>
<li>I have 19 out of 36 Type 2 Diabetes risk alleles. (<a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a>)</li>
<li>My combined risk of narcolepsy and Restless Leg Syndrome is 3.63x the average. (<a title="Interpretome" href="http://esquilax.stanford.edu/" target="_blank">Interpretome</a>)</li>
<li>I have a ton of alleles associated with an elevated risk for mental health issues (such as depression, bi-polar disorder, and schizophrenia), and being less likely than average to respond to certain antidepressant medications. (<a title="Promethease" href="http://snpedia.com/index.php/Promethease" target="_blank">Promethease</a>)</li>
</ul>
<p>A couple other things you can do with your 23andMe raw data involve submitting it to <a href="http://curetogether.com/lg.php?nextpage=/home/genome/" target="_blank">CureTogether</a> or <a href="http://gedmatch.com/" target="_blank">GEDmatch</a>, and cross-referencing your SNP data using the FireFox extension <a href="http://snptips.5amsolutions.com/" target="_blank">SNPTips.</a> If all four of your grandparents are from the same background, you can use <a href="http://dodecad.blogspot.com/" target="_blank">DIYDodecad</a>. (Mine aren&#8217;t, so I didn&#8217;t use it.)</p>
<p>By the way: my advice is not to pay full price for a kit, but to wait for it to go on sale because this seems to happen pretty frequently. The wait isn&#8217;t long for them to process your sample (of your spit inside a tube), it was only three weeks for me. &#8220;6-8 weeks&#8221; is the maximum time frame given.</p>
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		<item>
		<title>Two Thumbs Up</title>
		<link>http://juliesandburg.com/blog/2008/12/two-thumbs-up/</link>
		<comments>http://juliesandburg.com/blog/2008/12/two-thumbs-up/#comments</comments>
		<pubDate>Fri, 12 Dec 2008 14:15:32 +0000</pubDate>
		<dc:creator>Julie</dc:creator>
				<category><![CDATA[Politics]]></category>
		<category><![CDATA[Science]]></category>

		<guid isPermaLink="false">http://juliesandburg.com/blog/?p=105</guid>
		<description><![CDATA[I rub my hands together with glee as Ben Stein's dumb ass gets the smackdown by Roger Ebert over his dumb "intelligent design" movie, and jump in to help.]]></description>
			<content:encoded><![CDATA[<p>Although I was young, during my foray into evangelical Christianity as a child, I could not shake my doubt and critical thinking. &#8220;This doesn&#8217;t sound right,&#8221; I&#8217;d think often, but I mostly kept my thoughts to myself. I went along with it because my best friend, a fundamentalist Baptist, was into it. (I didn&#8217;t really feel like a fraud or hypocrite, though. I&#8217;ve always sort of kept part of myself under wraps. I would give up part of who I was to have friends or boyfriends. I&#8217;ve tried to stop doing that these days.)</p>
<p>This month, <a title="Roger Ebert" href="http://blogs.suntimes.com/ebert/2008/12/win_ben_steins_mind.html" target="_blank">Roger Ebert writes a review of Ben Stein&#8217;s &#8220;Expelled.&#8221;</a> But it&#8217;s not exactly a review, it&#8217;s more of a smackdown. Reading Ebert&#8217;s post made me remember when my friend sent me some Creationist materials from some presentation she saw. Amongst other things, it said that evolution was a lie made up by the devil and that it influenced, and was supported by, the Nazis. Huh. Interesting how we never hear about the latter from anyone but Creationists, perhaps because <a title="Hitler and evolution on SkepticWiki" href="http://www.skepticwiki.org/index.php/Hitler_and_evolution" target="_blank">it&#8217;s not true</a>. It sure does seem to be a staple of anti-evolution beliefs, though, a slippery slope from evolution to atheism to becoming Hitler (who identified as a Christian, but whatever):<br />
<span id="more-105"></span></p>
<blockquote><p>Toward the end of the film, we find that Stein actually <em> did</em> want to title it &#8220;From Darwin to Hitler.&#8221; He finds a Creationist who informs him, &#8220;Darwinism inspired and advanced Nazism.&#8221; He refers to advocates of eugenics as liberal. I would not call Hitler liberal. Arbitrary forced sterilization in our country has been promoted mostly by racists, who curiously found many times more blacks than whites suitable for such treatment.</p>
<p>He takes a field trip to visit one &#8220;result&#8221; of Darwinism: Nazi concentration camps. &#8220;As a Jew,&#8221; he says, &#8220;I wanted to see for myself.&#8221; We see footage of gaunt, skeletal prisoners. Pathetic children. A mound of naked Jewish corpses. &#8220;It&#8217;s difficult to describe how it felt to walk through such a haunting place,&#8221; he says. Oh, go ahead, Ben Stein. Describe. It filled you with hatred for Charles Darwin and his followers, who represent the overwhelming majority of educated people in every nation on earth. It is not difficult for me to describe how you made me feel by exploiting the deaths of millions of Jews in support of your argument for a peripheral Christian belief. It fills me with contempt.</p></blockquote>
<p>However, I have a couple bones to pick:</p>
<ul>
<li>Mr. Ebert missed a chance to educate readers on what &#8220;theory&#8221; means in a scientific context. Most Creationists don&#8217;t understand a meaning other than by its layperson definition. In science, a theory is knowledge based upon observable evidence. So for example, <a title="Evolution as a theory on Wiki" href="http://en.wikipedia.org/wiki/Evolution_as_theory_and_fact" target="_blank">evolution is both a theory and a fact</a>. By saying, &#8220;Evolution is just a theory&#8221; you could just as well say, &#8220;Gravity is just a theory.&#8221; Yet most Creationists don&#8217;t take issue with accepting gravity as the reason why things fall down.</li>
<li>He also missed a chance to explain how evolution does not cover how life originated on Earth; that study would be <a title="Abiogenesis on Wiki" href="http://en.wikipedia.org/wiki/Origin_of_life" target="_blank">abiogenesis</a>.</li>
</ul>
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